Merge branch 'release/0.15.0'

.rtd-environment.yml

@@ -0,0 +1,33 @@
+name: gimmemotifs
+channels:
+  - defaults
+  - bioconda
+  - conda-forge
+dependencies:
+  - configparser
+  - diskcache
+  - feather-format
+  - genomepy >=0.8.3
+  - jinja2
+  - logomaker
+  - matplotlib-base >=3.1.2
+  - ncurses
+  - numpy
+  - pandas >=1.0.3
+  - pillow
+  - pyarrow >=0.16.0
+  - pybedtools
+  - python >=3
+  - python-xxhash
+  - pyyaml >=3.10
+  - qnorm
+  - represent
+  - scikit-learn >=0.18
+  - scipy >=1.3.0
+  - seaborn
+  - statsmodels
+  - tqdm >=4.27.0
+  - xdg
+  - xgboost >=0.71
+  - sphinx_bootstrap_theme
+  - numpydoc

.travis.yml

@@ -21,8 +21,11 @@ before_install:
     fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b -p $HOME/miniconda -f
-  - export PATH=$HOME/miniconda/bin:$PATH
-  - conda config --set always_yes yes 
+  - source "$HOME/miniconda/etc/profile.d/conda.sh"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
   - if [ "$TRAVIS_OS_NAME" == "osx" ]; then ulimit -S -n 4096; ulimit -a; fi
 
 install:
@@ -34,7 +37,8 @@ install:
     else
       conda env create -q -f conda_env.osx.txt -n gimme;
     fi
-  - source activate gimme
+  - conda activate gimme
+  - conda list
   - python setup.py build && pip install -e .
 
 before_script:

CHANGELOG.md

@@ -13,6 +13,33 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Fixed
 
+## [0.15.0] - 2020-09-29
+
+### Added
+
+- Added additional columns to `gimme maelstrom` output for better intepretation (correlation of motif to signal and % of regions with motif).
+- Added support for multi-species input in `genome@chrom:start-end` format.
+- `gimme maelstrom` warns if data is not row-centered and will center by default.
+- `gimme maelstrom` selects a set of non-redundant (or less redundant) motifs by default.
+- Added SVR regressor for `gimme maelstrom`.
+- Added quantile normalization to `coverage_table`.
+
+### Removed
+
+- Removed the lightning classifiers and regressors as the package is no longer actively maintained.
+
+### Changed
+
+- Visually improved HTML output.
+- Score of `maelstrom` is now an aggregate z-score based on combining z-scores from individual methods using Stouffer's method. The z-scores of individual methods are generated using the inverse normal transform.
+- Reorganized some classes and functions.
+
+### Fixed
+
+- Fixed minor issues with sorting columns in HTML output.
+- `gimme motifs` doesn't crash when no motifs are found.
+- Fixed error with Ensembl chromosome names in `combine_peaks`.
+
 ## [0.14.4] - 2020-04-02
 
 ### Fixed

conda_env.dev.txt

@@ -3,12 +3,9 @@ configparser
 dinamo
 diskcache
 feather-format
-future
 gadem
-genomepy >=0.6.1
-ghostscript
+genomepy >=0.8.3
 homer
-icu=58
 ipywidgets  # Necessary for progress bar in Jupyter notebook
 jinja2
 logomaker
@@ -18,17 +15,16 @@ ncurses
 numpy
 prosampler
 pillow
-pyarrow
+pyarrow >=0.16.0
 pybedtools
 pysam
 python
 python-xxhash
 pyyaml >=3.10
-scikit-learn >=0.18
-scipy >=1.3.0
+qnorm
+scikit-learn >=0.23
+scipy >=1.4.1
 seaborn
-six
-sklearn-contrib-lightning
 statsmodels
 tqdm >=4.27.0
 trawler

conda_env.osx.txt

@@ -2,13 +2,13 @@ bedtools
 configparser
 diskcache
 feather-format
-future
 gadem
-genomepy >=0.6.1
+genomepy >=0.8.3
 ghostscript
 homer
 jinja2
 logomaker
+llvm-openmp
 matplotlib >=2.0
 meme >=5
 ncurses
@@ -21,19 +21,18 @@ pysam
 python
 python-xxhash
 pyyaml >=3.10
-scikit-learn >=0.18
-scipy <1.3.0
+qnorm
+scikit-learn
+scipy
 seaborn
-six
-sklearn-contrib-lightning
 statsmodels
 tqdm >=4.27.0
 trawler
 ucsc-bigbedtobed
 ucsc-genepredtobed
 weeder
 xdg
-xgboost >=0.71
+xgboost=0.72
 xxmotif
 
 # development-specific

conda_env.test.txt

@@ -0,0 +1,37 @@
+bedtools
+configparser
+dinamo
+diskcache
+feather-format
+gadem
+genomepy >=0.6.1
+ghostscript
+homer
+icu=58
+ipywidgets  # Necessary for progress bar in Jupyter notebook
+jinja2
+logomaker
+matplotlib >=2.0
+meme >=5
+ncurses
+numpy
+pillow
+prosampler
+pyarrow
+pybedtools
+python >=3.8
+python-xxhash
+pyyaml >=3.10
+qnorm
+scikit-learn >=0.18
+scipy <1.3.0
+seaborn
+statsmodels
+tqdm >=4.27.0
+trawler
+ucsc-bigbedtobed
+ucsc-genepredtobed
+weeder
+xdg
+xgboost >=0.71
+xxmotif

conda_env.txt

@@ -1,39 +1,35 @@
-bedtools
 configparser
 dinamo
 diskcache
 feather-format
-future
 gadem
-genomepy >=0.6.1
+genomepy >=0.8.3
 ghostscript
 homer
-icu=58
 ipywidgets  # Necessary for progress bar in Jupyter notebook
 jinja2
 logomaker
-matplotlib >=2.0
-meme >=5
+matplotlib-base >=3.1.2
+meme >=5.1.1
 ncurses
 numpy
+pandas >=1.0.3
 pillow
 prosampler
-pyarrow
+pyarrow >=0.16.0
 pybedtools
 pysam
-python
+python >=3
 python-xxhash
 pyyaml >=3.10
+qnorm
 scikit-learn >=0.18
 scipy <1.3.0
 seaborn
-six
-sklearn-contrib-lightning
 statsmodels
 tqdm >=4.27.0
 trawler
 ucsc-bigbedtobed
-ucsc-genepredtobed
 weeder
 xdg
 xgboost >=0.71

data/templates/sortable/sortable-theme-slick.css

@@ -1,6 +1,7 @@
 /* line 2, ../sass/_sortable.sass */
 table[data-sortable] {
-  font-size: 80%;
+  font-family: 'Nunito Sans';
+  font-size: 90%;
   border-collapse: collapse;
   border-spacing: 0;
 }